Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

By E. N. Nolte-‘t Hoen, H. Buermans, M. Waasdorp, W. Stoorvogel, M. Wauben, P. '. ’t Hoen. Nucleic Acids Research, 2012

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Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8345aa24453e6211b82bc1426464c565b553070f

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Citations in the corpus

Exosomes and other extracellular vesicles in host–pathogen interactions (2014, unknown): “More recent studies have identified other non-coding RNAs in exosomes, but limited amounts of DNA or ribosomal RNA [57].”
SORTING IT OUT: REGULATION OF EXOSOME LOADING (2014, background): “Exosomes are also enriched in small RNA species, including vaultRNA, tRNA and miRNAs [11].”
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Extracellular vesicles: Exosomes, microvesicles, and friends (2013, background): “…the release of MVs and change the protein composition thereof in response to activation by lipopolysaccharides (Obregon et al., 2006; Nolte-’t Hoen et al., 2012c), whereas peptide-loaded immature dendritic cells were stimulated to release exosomes in response to their interaction with T…”
Introduction to Extracellular Vesicles: Biogenesis, RNA Cargo Selection, Content, Release, and Uptake (2016, unknown): “In addition to the commonly known RNA species, such as mRNAs, miRNAs, and rRNAs, long and short non-coding RNA, tRNA fragments, piwi-interacting RNA, vault RNA, and Y RNA have been found in EVs (Crescitelli et al. 2013; Cheng et al. 2013; Huang et al. 2013; Ogawa et al. 2013; Xiao et al. 2012; Nolte”
Tetraspanins in Extracellular Vesicle Formation and Function (2014, background): “RNA SORTING TO EVs Exosomes also contain a selected composition in small RNAs (vaultRNA, tRNAs, and miRNAs) (103) and specialized mechanisms are involved in their recruitment and loading to EVs (104).”
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